In recent years, fruits of Torreya grandis enjoy great popularity, now, how to increase fruit yield and improve fruit quality, especially the concentrations of micronutrients in fruits are essential for T. grandis cultivation. Selenium is the essential element for the biosynthesis of selenoproteins, and lack of it is related to some human diseases. In the present study, T. grandis seedlings were planted in plastic pots, powder of selenium rock was applied in the cultivation substrate, and root endophytic fungus Piriformospora indica was inoculated with T. grandis seedlings. The results showed the fungus could infect the roots of T. grandis seedlings, and the inoculation increased the total root length, surface areas, root volumes and the numbers of the first-order roots on the second-order roots by 12.69%, 16.26%, 20.81% and 10.93%, respectively. However, the inoculation did not affect the specific root length and root tissue densities of T. grandis seedling roots. The inoculation significantly increased the net photosynthesis rates, stomatal conductance, intercellular CO2 concentrations and transpiration rates by 92.92%, 6.16 times, 47.67% and 2.36 times, respectively. And the inoculation significantly increased the light use efficiency (88.62%) and reduced the water use efficiency (84.28%). Compared with non-inoculated seedlings, inoculated seedlings showed significantly higher total biomass accumulation and total selenium concentrations in the leaves by 36.94% and 1.68 times, correspondingly. The result suggested that the root endophytic fungus P. indica might be used in cultivation of T. grandis for selenium biofortification in the fruits.